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The Looy Lab paleo detectives: Dori and Cindy at the NMNH

Cissites

A Cissites harkerianus leaf from Ellsworth County, Kansas, collected by Charles Sternberg in the late 1800s, and identified by Leo Lesquereux. Specimen from the Department of Paleobiology, National Museum of Natural History. (photo by Dori Contreras)

Tuesday morning, February 12, 2013, Dori Contreras and Cindy Looy woke before dawn to catch a cross-country flight to Washington, DC, for a two-week visit to the Smithsonian’s National Museum of Natural History (NMNH). Originally, Cindy was going to attend a biannual workshop of the Evolution of Terrestrial Ecosystem Program. However, after Dori obtained a Sigma Xi grant to study a fossil leaf collection housed in the NMNH’s paleobotanical collections, they teamed up and turned it into a joint research excursion filled with an array of activities.

Dori: My main goal was to collect data for a study on the leaf characteristics of early flowering plants from a warm wet climate approximately 100 million years ago. And just to clarify, what I mean by "data" is photographs — lots and lots of high-resolution photographs of individual fossil leaves preserved in rock. The specific fossils that I was interested in come from the Fort Harker locality in Kansas. They were collected over a roughly 30-year period (1860s through 1890s) as a part of the US Geological Survey’s explorations of the geology of the Western Interior of the United States.

I wasn’t exactly sure how many specimens I would find in the museum "stacks," which consist of rows and rows of floor-to-ceiling cabinets filled with drawers of fossils. Based on Leo Lesquereux’s publications from the late 19th century, I was expecting somewhere around 100 specimens. However, after two days of opening wooden drawers I located just over 300 Fort Harker specimens! Many have never been figured or mentioned in publications, and most have not been reevaluated in over 100 years.

Dori with the camera setup

Dori photographing the Cretaceous Fort Harker flora. (photo by Cindy Looy)

I knew that it would be a major task to photograph them all in the detail needed for study, so I went right to work. The museum's imaging room had an impressive setup of top-notch, stand-mounted cameras connected to computers for remote shooting. Most of my time was spent carting specimens back and forth between the stacks and imaging room and doing nonstop photography. The trickiest part of imaging for data collection was getting the lighting angle and brightness just right to pick up the three-dimensional (and often obscure) features of each leaf. At least magnification wasn't an issue — the resolution of the camera I used was so high that a microscope was not necessary!

Inga

Inga cretaceum, another fossil leaf collected by Charles Sternberg and identified by Leo Lesquereux. Specimen from the Department of Paleobiology, National Museum of Natural History. (photo by Dori Contreras)

Ultimately, I was able to photograph almost every specimen in the collection, totaling a whopping 50 gigabytes of images. Now I look forward to the next tasks: naming and organizing all those files, followed by detailed measuring of key ecological leaf characteristics for each specimen. Luckily ,a new Undergraduate Research Apprentice Program (URAP) student just joined "Team Contreras." We hope this study will provide insight into the structure and function of plant communities in warm, wet climates during the early radiation of flowering plants.

Cindy: Last year, members of the NMNH's Evolution of Terrestrial Ecosystem Program received good news from NSF: their Research Coordination Network proposal, "Synthesizing deep time and recent community ecology," was funded. This means that over the next five years a group of paleo- and "extant" ecologists will meet semiannually to study the assembly and disassembly of biological communities in the past and present. Attending this winter's edition of our meeting series was my main goal of this museum trip. Our workshop consisted of three days of presentations, data gathering and subsequent analyses in a friendly and inspiring atmosphere.

Workshop attendees

The NMNH’s Evolution of Terrestrial Ecosystems Program workshop attendees. Cindy is ninth from the left. (photo by Dori Contreras)

It is always a treat to return to the NMNH, smack in the middle of the National Mall in DC. From 2004 to 2008 I worked as a research fellow in the Paleobiology Department of this bigger sister of the UCMP and being at the NMNH always instills a special feeling. It could be the 325,000 square feet of exhibition space, the 20,000 daily visitors from all over the globe, or the 126,000,000 documented specimens in the museum's collections. Perhaps it is the illusion of being in the "center of the world," with the close proximity of the NMNH to the White House. But still, I know how lucky I am to be at the west coast equivalent of the NMNH. The UCMP public exhibits may be primarily online, but with the Department of Integrative Biology, the UCMP boasts something that the NMNH lacks altogether and something that presidential fly-bys can never compensate for: a pack of fabulous graduate and undergraduate students!

Outside of the meeting I had plenty of time to catch up with friends and work with former colleagues. Fellow-paleobotanist Bill DiMichele and I spent quite a bit of time in the museum's paleobotany collections. During the past 20 years, Paleozoic paleobotanists from the NMNH (Bill DiMichele, Dan Chaney, and Serge Mamay) have intensively sampled latest Pennsylvanian, Early Permian and Middle Permian sites in Texas. More than 360 collections of compression fossils were assembled using sampling strategies appropriate for the reconstruction of plant communities. Bill and I pulled out numerous conifers for morphotyping. We are trying to get a grip on how diverse early Permian Euramerican forests were, and how seed-plant dominated assemblages changed through time. Working our way through all the cabinets took quite some time, but that's nothing compared to all the imaging and measuring that still needs to be done. Ah well, that’s what is great about being a scientist: the work is never completed. Every question answered raises plenty of new, interesting questions.

Bill and Cindy

Cindy and Bill DiMichele working in the paleobotanical collections. (photo by Dori Contreras)

Both: Additionally, we got to present our work to east coast paleontologists and geologists at the annual Penn-Smithsonian Geobiology Symposium. It's always good to foster cross-talk on the continental scale and represent the paleontological force that is the UCMP!

Cindy and Dori sample pie

If you ever find yourself in DC, we highly recommend breakfast at Paul's French bakery ("Bonjour Madame!"). Here we test some of their pies for Cindy’s birthday. (photo by Bill DiMichele)

Reports from Regatta: Two Cal Alumni and the USGS Menlo Park Collection

Nelson letter and envelope

The letter from Cliff Nelson to Warren Addicott.
 

As undergraduate work-study students recataloging the United States Geological Survery (USGS) Menlo Park Invertebrate collection at the UCMP, we've come across the names Nelson and Addicott time and time again in extensive database entries or on the original, yellowing locality cards paired with each specimen. The names of the paleontologists and geologists responsible for collecting these fossils in the Menlo Park collection are largely unknown to us, but found immersed within the aging drawers of the invertebrate fossils were several curious and antiquarian documents that have brought these names to life. One recently discovered letter, written by UC Berkeley alumnus Cliff Nelson records his activities in the collections during the summer of 1974.

In the letter, Nelson discusses his dissertation work that focused on migration patterns of Neptunea, a large sea snail indigenous to the North Pacific. While studying the migration traces of Neptunea through the North Pacific and to the North Atlantic and California Current, Nelson proposed to elevate Neptunea beyond the level of subgenus. His dissertation interpreted Neptunea as a genus, with the inclusion of 56 named species — half of which are extinct. The letter goes on to explain Nelson's use of the Menlo Park collection and the late nights he spent scavenging through the collections, searching for invertebrate specimens to support his dissertation.

The letter also delivers some insights on other individuals who played an important role in Nelson's research. Warren Addicott, the recipient of Nelson's letter (and another popular name found often in the Menlo Park Collection), obtained his doctorate at UC Berkeley in 1956 and led a distinguished scientific career at the US Geological Survey. The letter concludes with Nelson's gracious thanks to Addicott for his help with his dissertation and an acknowledgment to Dr. Stearns McNeil, another familiar name associated with the Menlo Park collection and the USGS.

After receiving his Ph.D. from UC Berkeley in 1974, the year the letter was written, Nelson went on to publish over fifty articles in refereed journals and books. His work primarily focused on the history of scholarship, ideas, and institutions in natural sciences. Currently, Nelson works as a geologist and historian at the USGS. In 2011 he received the Friedman Distinguished Service Award from the Geological Society of America's History and Philosophy of Geology Division.

Letters such as this one help us discover the identities of the names we come upon so frequently. This is just one of many documents that shines light on the Menlo Park collection and allows us to reconstruct the UC Museum of Paleontology's historic and scientific past.

Neptuneidae specimens

USGS gastropod specimens (Family Neptuneidae) studied by Nelson during the course of his doctoral study at UC Berkeley. Left: A specimen from USGS Cenozoic Locality M863 Pliocene, Gubick Formation of Alaska, Colville River. Right: A specimen identified by Nelson as Beringius beringii; from USGS Cenozoic Locality M860 Pleistocene, Gubik Formation near Point Barrow village, Alaska. Both specimens were collected by John O'Sullivan pre-1960.

The Looy Lab paleo detectives

Solving the mysteries of the past and present one rock at a time

East of the Berkeley campus, we see the beautiful, green Berkeley Hills, the golden letter "C" and a somewhat classy-looking, dome-shaped building on the Lawrence Berkeley National Laboratory campus. This houses the ALS, or Advanced Light Source. Personally, I find the name a bit silly because it doesn't seem to capture the awesomeness of this giant machine. It's like calling the Space Shuttle a Progressive Flying Tool.

synchotron at LBL

Photo from newscenter.lbl.gov

The ALS is a synchrotron, a particular type of particle accelerator. The particles are sped up by a shifting magnetic field within a closed circuit. The shape of this circuit is an almost circular polygon and since the building was specifically designed for the synchrotron, the building is round. But what happens inside?

Each time when the particle beam is bent at each of the polygon's corners, light is produced — primarily ultraviolet and x-rays. The x-rays are not your ordinary dental office x-rays, but much "harder" x-rays. Unlike the relatively harmless photo at the tooth doctor, this beam would kill you before you could say "¿qué?"

But what can paleontologists and paleobotanists do with this advanced light? Hard x-rays allow us to see fossils while they are still inside the rock. This means that you don't have to crack open the rocks, clear away rock matrix and run the risk of damaging precious fossils. In some cases, the material is simply too fragile to be prepared; it would not hold up. Scanning the rock allows us to make 3D reconstructions of fossils hidden inside the rock without damaging them.

We've been scanning all kinds of really old fossils: horsetails from the Carboniferous (~300 million years ago, or Ma), kelp holdfasts from the Oligocene (~30 Ma), tiny (3 mm or ~1/8 inch) and not so tiny (7 cm or ~2¾ inch) pine cones, early land plants from the Devonian (~390 Ma), and pollen cones of extinct redwoods from the Cretaceous (~70 Ma). The size of the fossils is limited by the size of the protective shielding enclosure that keeps the scientists safe while using these lethal x-rays.

Because the cyclotron basically runs 24/7, the scanning time slots are generally 24 hours long and scanning rocks can take a while. Here's the general process that we go through for each scan:

Cindy and Ivo

Left: First, we select a fossil. Right: Then we mount it on a stand (improvising a la MacGyver). These and the rest of the photos are by Cindy Looy and Dori Lynne Contreras.

Orienting a fossil on the stand

Next we orient the fossil on the stand just right to get the best quality scan of the target specimen (which surprisingly takes a bit of work and "expert guess-timation").

The hutch

Once ready, the mount and fossil are placed in a "hutch" made of radiation shielding. Left: This is the hutch, a big container that protects everyone around from the harmful x-rays. Right: Inside the hutch there is a normal optical camera (at ~9 o'clock), the stand on which the fossil is mounted, and the x-ray detector (the big black box at the right).

The hutch doors and camera

To start the scanning process a number of safety procedures have to be followed, otherwise the beamline will not open. Left: The doors of the hutch have to be closed, and while an ominous alarm sounds, you have to press certain buttons to actually allow the x-ray to come into the hutch. Once it does, a red rotating emergency light comes on and the doors cannot be opened. Right: Once the sample is in the hutch we use the normal camera to focus in on the sample.

Adjusting the settings and set to go

Left: As each fossil sample is different, adjustments to the settings are needed. For instance, thicker rocks generally need a higher dose of x-rays than thin ones. Right: And we are good to go! It's scanning time!

Waiting for the scan to finish

And then, we wait …

Data analysis and celebration

Left: Actually, there is not a whole lot of sitting about going on, because the data that the x-ray collector gathers has to be analyzed. This takes up quite a bit of time (note the ridiculous amount of caffeine) and a LOT of computing power. Luckily, the computers at Lawrence Berkeley National Lab are up to the task! Right: Then we celebrate our success!

Darwin Day Roadshow

Lisa's presentation

Lisa White makes her presentation to Mrs. Ball's 7th grade class at the Urban Promise Academy in Oakland. Photo by Alison Ball.
 

It is not unusual to see evolutionary biologists around the world involved in celebration activities on February 12th — the reason? Charles Darwin's birthday! UCMP and the National Evolutionary Synthesis Center (NESCent) are no exception and this year the activities overlapped. Two years ago, NESCent initiated the Darwin Day Roadshow in order to bring evolutionary science to schools and museums around the country. This year, Lisa White was asked by NESCent to bring the Roadshow to Urban Promise Academy, a small Oakland Unified School District middle school serving students in the Fruitvale neighborhood of Oakland, CA. Presenting to Ms. Alison Ball's 7th grade classroom on February 15, 2013, Lisa highlighted research at the UCMP, profiling examples of evolution from the Understanding Evolution website, while conveying why the science of evolution is important and relevant.

To the enjoyment of the students, Lisa brought in an array of fossils for the students to touch and see the tangible evidence for evolution up close. Lisa also spoke about her own education and training, what it is like to be a paleontologist, and how she came to work at the UCMP. Lisa said "the students were such an inspiration and their enthusiasm and eagerness to learn more about paleontology suggests the next generation of potential scientists are alive and well in classrooms like Urban Promise Academy."

Caldwell's rare octopus research makes headlines

Roy Caldwell has been working with Richard Ross of the California Academy of Sciences to study a rare, beautiful, and so far unnamed species of octopus. Their work, along with some of Roy's photos, is the subject of a feature article in the San Francisco Chronicle.

New bone histology book from UCMP and UC Press

The University of California Press has just published Bone Histology of Fossil Tetrapods: Advancing methods, analysis, and interpretation. The book represents the proceedings of an NSF-sponsored workshop and is the first comprehensive summary of the field of fossil bone histology. The twelve authors of the various chapters cover topics ranging from basic bone biology to calculating and analyzing the evolution of growth rates in bones, in addition to step-by-step instructions for setting up a hard tissue histology lab and processing specimens.

The microstructure of bone has a great deal to tell us about the biology of ancient vertebrates. The patterns of how bone tissue was deposited and the configuration of the blood canals in the bone provide a very good idea of how fast the animal was growing, and how its growth regime changed through life. Growth lines, deposited annually like tree rings, help us to calculate how old animals were when they died and even when they matured sexually. These data in turn give us information about life history strategies and metabolic regimes.

UCMP alum Andrew Lee and grad student Sarah Werning were two of the many contributors to the volume who have benefited from studying UCMP’s fossil collections. UCMP researchers have been in the forefront of fossil bone histology for decades, and our histology lab continues to be one of the most active research areas of the Museum. The book was edited by Kevin Padian of UCMP and Ellen-Thérèse Lamm of the Museum of the Rockies.

Cataloging the Archives: Three Fine Trikes

Another in a series of blog posts relating to the museum's "cataloging the archives" project

Ask children what their favorite dinosaurs are, and it's almost guaranteed that Triceratops (refer to them by their nickname, Trikes, and you'll earn tons of street cred) will be on the list. The three-horned, frilled wonder is one of the most recognizable creatures of the Cretaceous. Many a visitor has walked by the Triceratops display here in the Valley Life Sciences Building's Marian Koshland Bioscience and Natural Resources Library. Over time, the display has grown, not only to include more skulls, but to tell a bigger story. Now there are three skulls in the display, each with its own interesting history, but when taken together the tale reaches almost epic status (okay, "impressive" status).

Ruben at locality2

 

The largest of the skulls is UCMP specimen 113697, also known as "Ruben's Trike." While on a UCMP field expedition to Montana and neighboring states in July, 1970, paleontology graduate student John Ruben (now a professor in the Department of Zoology, Oregon State University) discovered the skull in the roughly 68-million-year-old rocks of the Hell Creek Formation of eastern Montana. The Hell Creek is one of the most fruitful formations for Trike discoveries, and if you've done field work in the Upper Cretaceous of Montana and haven't come across some part of a Triceratops, you're doing something wrong.

John Ruben (black hat) at his "Ruben's Trike" locality, V75046, where the skull, UCMP 113697, was found, McCone County, MT.

 

The medium-sized Triceratops skull, UCMP 136306, is also known as the "McGuire Creek Trike" since its discovery in badlands of the Hell Creek Formation exposed in the vicinity of this creek drainage in McCone County, Montana. Weathered fragments of bone or "float" from the skull were first sighted by paleontology undergraduate Wayne Thomas in the summer of 1984 on a UCMP field research trip. Further excavation by UCMP Assistant Director Mark Goodwin and crew that summer confirmed Wayne's discovery was a nearly complete juvenile Triceratops skull. The find was exciting in itself, but it also helped fill in some holes in the understanding of Triceratops growth from baby to adult (known as ontogeny) and generated new research by Goodwin, his colleague Jack Horner from the Museum of the Rockies, and their students. For more information on Trike ontogeny, stay tuned for a future blog entry centered on this exact topic.

The smallest of the Trike skulls, UCMP 154452, was found in the Hell Creek Formation (see a trend?) of Montana by long-time UCMP field associate and collector, Harley J. Garbani, in 1995.

When Harley came across the specimen, he first identified it as a possible pachycephalosaur because the tiny brow horn so closely resembled the horns and knobs seen ornamenting the back of the skulls of pachycephalosaurs, or "dome-headed" dinosaurs. Being a very young individual, likely less than a year old, the skull showed features not seen before on a Trike, was very delicate, and in many pieces. Trying to determine what some specimens are from many fragments can be a tedious and insanity-inducing ordeal (ask any fossil preparator).

After corresponding with, and providing pictures to, Mark Goodwin and Professor Bill Clemens, the specimen was correctly identified and also keyed Goodwin into finding a near identical isolated postorbital or "brow" horn from the skull of another baby Triceratops in the UCMP collections.

Baby trike collage 1

Left: HJG 1030, the Baby Trike Site. Photo by Bill Clemens. Top right: A portion of Harley Garbani's field notes. He crossed out "Dome-Head" (i.e., pachycephalosaur) after learning it was a baby Triceratops! Bottom right: An excerpt from a letter that Harley wrote to Bill Clemens. He knew he had something important, and very quickly corresponded with the right parties to learn why. Image courtesy of Bill Clemens.

Baby trike collage2

Top left: Photo of a table top covered with the bones of the baby Trike skull discovered by Harley Garbani. Bottom left: Reconstruction of baby Trike. Photo by Dave Smith. Right: Assistant UCMP Director and dinosaur paleontologist Mark Goodwin working on the baby Triceratops skull. It was prepared, molded, and cast so that an accurate reconstruction (on exhibit in the Biosciences Library) could be made available for research and display. Images of Mark Goodwin and skull bones courtesy of Bill Clemens.

 

Harley’s discovery was a game-changer since it was, and still is, the smallest Triceratops skull and by inference, the youngest yet known. Together, these three skulls tell a story about skull development and growth in a dinosaur that was named by O.C. Marsh of the Yale Peabody Museum over 120 years ago!

UCMP paleontologists are still discovering new things about this very popular dinosaur. Fossils are often known for whatever novel thing they can tell us, but sometimes a seemingly small and, at first, very fragmentary fossil becomes significant when studied in the context of other fossils and when you hear the story behind its discovery. These Triceratops skulls are interesting on both counts!

Understanding Science in the video spotlight

The California Academy of Sciences produced a video that uses UCMP's Understanding Science website's How Science Works flowchart to map the discovery of a new spider family. UCMP Education and Public Programs team leaders Judy Scotchmoor and Lisa White have starring roles! Watch the video at Science360.

Lucy Chang captures honors at the International Biogeography Society meeting

IB Students Lucy Chang and Brad Balukjian celebrate their poster success! Photo courtesy of George Roderick.

UCMP grad student, Lucy Chang, received recognition for her student poster at the recent International Biogeography Society meeting in Miami. She was one of two winners in the category of Conservation and Global Change. There were more than 300 student posters dispersed among four categories and only two winners in each category. Lucy’s poster focused on the use of the fossil record to understand how biotas are established in epeiric (epicontinental) seas. See abstract below.

Abstract: Building up the biota in novel environments: insights using the fossil record of epeiric seas
Throughout the Phanerozoic, times of rising sea level were often accompanied by the development of shallow seas on the continents. These epeiric seas formed relatively rapidly in geologic time and differed physically from open marine habitats, with shallower depths and altered salinity, temperature, and circulation. The build-up of diversity within these new habitats must result from one or more of the following processes: uninhibited dispersal of open marine taxa, limited dispersal with ecological filtering of open marine taxa, and one or more rounds of in situ speciation. The paleontological record allows discrimination between these processes and additionally chronicles any accompanying anagenesis. Despite the extensive representation of epeiric seas in the fossil record, little has been done to characterize and determine the source of epeiric biotas. My focus is on ammonites in the Late Cretaceous, characterized by high sea levels and inland flooding, including creation of a seaway across North America between the Arctic Ocean and the Caribbean Sea. Ammonites are an ideal study group because they are fast evolving, abundant and well preserved — features that allow for fine temporal and spatial control. Using geographic and temporal distributions and body size data for over 500 species of ammonite, I present spatial patterns in diversity and ecology of Cretaceous ammonites across epeiric and non-epeiric habitats to determine the relative importance of the various processes that build diversity in novel environments.

An evening with Neil Shubin

UCMP has partnered with the Jewish Community Center of San Francisco's Arts & Ideas series to present a lecture by Neil Shubin on Wednesday, January 16.

Paleontologist and evolutionary biologist Neil Shubin is famed for discovering the fossilized Tiktaalik roseae, the missing link between ancient sea creatures and land dwellers. His bestselling book, Your Inner Fish, shows parallels between human anatomy and the structures of the fish that first wriggled landward 375 million years ago. In his new book, The Universe Within, he goes one step further, explaining how the universe’s 14-billion-year history is reflected in our bodies, right down to our molecules. Neil Shubin is a professor of Organismal Biology and Anatomy at the University of Chicago and a Fellow of the California Academy of Sciences. Academy Fellows are a distinguished group of eminent scientists recognized for notable contributions to one or more of the natural sciences.

Get more event/ticket information.